4XB6 | pdb_00004xb6

Structure of the E. coli C-P lyase core complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d4xb6f_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PhnH-like	PhnH-like	automated matches	(Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ],	SCOPe (2.08)
B	d4xb6b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PhnH-like	PhnH-like	automated matches	(Escherichia coli str. K-12 substr. MG1655 ) [TaxId: 511145 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	PhnH-like	8034005	3001133	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PhnH-like	8034005	3001133	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	PhnJ_N	e4xb6H2	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnJ_N	ECOD (1.6)
H	PhnJ_C	e4xb6H1	A: few secondary structure elements	X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	T: C-P lyase subunit PhnJ C-terminal Zn-binding domain	F: PhnJ_C	ECOD (1.6)
D	PhnJ_N	e4xb6D1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnJ_N	ECOD (1.6)
D	PhnJ_C	e4xb6D2	A: few secondary structure elements	X: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	H: C-P lyase subunit PhnJ C-terminal Zn-binding domain (From Topology)	T: C-P lyase subunit PhnJ C-terminal Zn-binding domain	F: PhnJ_C	ECOD (1.6)
G	PhnI_N	e4xb6G2	A: alpha arrays	X: RuvA-C	H: C-P lyase subunit PhnI N-terminal domain (From Topology)	T: C-P lyase subunit PhnI N-terminal domain	F: PhnI_N	ECOD (1.6)
G	PhnI_C	e4xb6G1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnI_C	ECOD (1.6)
C	PhnI_N	e4xb6C2	A: alpha arrays	X: RuvA-C	H: C-P lyase subunit PhnI N-terminal domain (From Topology)	T: C-P lyase subunit PhnI N-terminal domain	F: PhnI_N	ECOD (1.6)
C	PhnI_C	e4xb6C1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnI_C	ECOD (1.6)
F	PhnH	e4xb6F1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnH	ECOD (1.6)
B	PhnH	e4xb6B1	A: a/b three-layered sandwiches	X: PhnH-like (From Topology)	H: PhnH-like (From Topology)	T: PhnH-like	F: PhnH	ECOD (1.6)
E	PhnG	e4xb6E1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnG	ECOD (1.6)
A	PhnG	e4xb6A1	A: a+b two layers	X: C-P lyase subunit PhnG (From Topology)	H: C-P lyase subunit PhnG (From Topology)	T: C-P lyase subunit PhnG	F: PhnG	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (4.3.0)
B	3.40.50.11310	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Bacterial phosphonate metabolism protein PhnH	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, H	PF06007	Phosphonate metabolism protein PhnJ (PhnJ)	Phosphonate metabolism protein PhnJ	-	Family
C, G	PF05861	Bacterial phosphonate metabolism protein (PhnI) (PhnI)	Bacterial phosphonate metabolism protein (PhnI)	-	Family
B, F	PF05845	Bacterial phosphonate metabolism protein (PhnH) (PhnH)	Bacterial phosphonate metabolism protein (PhnH)	-	Family
A, E	PF06754	Phosphonate metabolism protein PhnG (PhnG)	Phosphonate metabolism protein PhnG	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, H	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	lyase activity catalytic activity carbon phosphorus lyase activity alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
C, G	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI	alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
B, F	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex
A, E	Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG	alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity transferase activity catalytic activity phosphotransferase activity, for other substituted phosphate groups transferase activity, transferring phosphorus-containing groups	organic phosphonate metabolic process oxoacid metabolic process metabolic process cellular process small molecule metabolic process organic acid metabolic process phosphorus metabolic process localization transport organic phosphonate transport establishment of localization inorganic anion transport catabolic process organic phosphonate catabolic process	protein-containing complex catalytic complex carbon phosphorus lyase complex transferase complex, transferring phosphorus-containing groups alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex transferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, H	IPR010306	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase	Family
C, G	IPR008773	Phosphonate metabolism protein PhnI	Family
B, F	IPR038058	PhnH-like superfamily	Homologous Superfamily
B, F	IPR008772	Bacterial phosphonate metabolism, PhnH	Family
A, E	IPR009609	Phosphonate metabolism PhnG	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
D	alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase M-CSA #949	This radical SAM (AdoMet) enzyme is part of the C-P lyase complex, which is responsible for processing phophonates into usable phosphate. The enzyme from the bacterium Escherichia coli can act on additional alpha-D-ribose phosphonate substrates with different substituents attached to the phosphonate phosphorus (e.g. alpha-D-ribose-1- (N-(phosphonomethyl)glycine)-5-phosphate and alpha-D-ribose-1-(2-N- acetamidomethylphosphonate)-5-phosphate).	Defined by 5 residues: GLY:D-32CYS:D-241CYS:D-244CYS:D-266CYS:D-272 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 4.7.1.1 (PDB Primary Data)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.